Immense evolutionary pressure has driven bacteria to innovate a diverse arsenal of immune systems that defend against parasitic mobile genetic elements, including bacteriophages and plasmids. The study of these systems has proven extraordinarily fruitful for biotechnology: CRISPR-Cas9, originally discovered as a bacterial defense mechanism, has revolutionized genome editing and demonstrated the transformative potential of mining bacterial immunity for molecular tools.
\r\nYet the diversity of bacterial defense extends far beyond CRISPR. Bacteria have evolved numerous strategies to recognize and destroy foreign DNA, many of which remain poorly understood at the mechanistic level. A central question is how these systems distinguish self from non-self — and how the underlying molecular logic of DNA targeting is encoded in protein structure and biochemistry. We combine cryo-electron microscopy, quantitative biochemistry, and in vivo genomics to characterize newly discovered defense systems and dissect their targeting mechanisms. This work is revealing unexpected principles of foreign DNA recognition, with implications both for our understanding of bacterial immunity and for the development of next-generation biotechnological tools for genome editing and beyond.
Thesis Directors: Prof. A. Chiesa, Prof. M. T. Göös
\r\nComputer and Communication Sciences doctoral program
\r\nThesis Nr. 11413
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Thesis Director: Prof. N. Geroliminis,
\r\nCivil and Environmental Engineering doctoral program
\r\nThesis Nr. 11281
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Two-dimensional (2D) materials have emerged as a versatile platform at the intersection of fundamental physics and applied science. Their atomically thin nature gives rise to distinctive electronic and optical properties, while simultaneously enabling them to function as highly sensitive, readily integrable probes of their local environment. Advanced optical techniques, such as super-resolution microscopy, have opened new opportunities to interrogate these materials at the nanoscale, providing optical access to individual defect behaviors, exciton diffusion and recombination dynamics, and charge transport pathways. Such approaches not only deepen our understanding of intrinsic material behavior but also position 2D systems as powerful sensors capable of resolving local dielectric variations, electric and magnetic fields, and other environmental perturbations.
\r\nCentral to this work is hexagonal boron nitride (hBN), a transparent, wide bandgap semiconductor that serves as a host for optically active defects. These defects function as reaction centers, single-photon emitters, and spatially resolved nanoscale sensors that can be readily integrated into electronic and photonic architectures. Owing to its optical transparency, chemical stability, and compatibility with diverse material platforms, hBN provides an exceptional foundation for optical sensing. Building upon this foundation, we explore material properties and present new methods for spatially resolved in situ optical imaging with hBN to advance dynamic, wide-field optical sensing.
\r\nWe investigate a previously reported class of emitters that arise from interactions between native hBN and organic solvents. These emitters are believed to originate from defect sites that bind transiently to solvent molecules. To study their behavior, we develop a platform for imaging the dynamics of these transient emitters while varying the electrochemical potential and applying electric fields with controlled orientations. By tracking the spectra of individual emitters, we enable multiplexed measurements that allow spatially resolved electrochemical imaging. Through systematic analysis, we rule out modulation mechanisms based on direct electric field effects or charge transfer. Instead, we identify a mechanism driven by changes in H⁺ concentration, which is modulated during the oxidation of trace water present in the solvent. This finding opens the possibility of using this platform for sensitive detection of H⁺ and trace water in methanol fuel cells, where such species critically influence operational efficiency.
\r\nIn the final part of the thesis, we focus on a well-characterized spin defect in hBN, the negatively charged boron vacancy, and explore strategies to enhance its photoluminescence (PL) through heterostructure engineering that facilitates energy and exciton transfer. We demonstrate the coupled structure’s improved utility in optical magnetometry compared to the defect by itself and discuss how improvements in PL could advance the development of wide-field optically detected magnetic resonance (ODMR) imaging using this spin defect. Using a defect in hBN would leverage 2D materials’ exceptional sensing capabilities and planar integrability.
\r\nOverall, this thesis aims to highlight the strengths of integrating 2D materials with optical sensing and to develop transferable techniques for introducing controlled stimuli, such as electrochemical potentials, electric fields, or electromagnetic waves, with high fidelity and minimal artifacts. These advances not only demonstrate the potential of hBN as a versatile sensing platform but also establish methodologies applicable to a wide range of low-dimensional material systems.
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\r\nFor zoom:
\r\n Meeting ID: 611 3428 2068 Passcode: 952027
Thesis Director: Prof. W. A. Jakob,
\r\nComputer and Communication Sciences doctoral program
\r\nThesis Nr. 11469
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\r\nTo take part in the public defense, please contact directly the speaker